The diversity and ecology of symbiotic eukaryotes remain consummately uncharacterized. While previous studies on the associated eukaryotic communities of vertebrates have reported low levels of diversity relative to both sympatric prokaryotic and free-living eukaryotic communities, these findings may be more indicative of differences in the methodologies used to characterize these communities than of ecological differences between these systems. To assess the potential for such hidden diversity within primates, we utilize a novel Illumina sequencing approach to characterize eukaryotic diversity within the feces of wild long-tailed macaques (Macaca fascicularis) on two islands in southeast Asia (N=45): Singapore and Bali, Indonesia. We report levels of eukaryotic diversity higher than those previously reported from the feces of primates and comparable to many free-living systems. All five eukaryotic super-groups were represented and several taxonomic groups were found to be common across all samples, suggesting the existence of a core eukaryotic community. Despite these commonalities, differences in eukaryotic gut assemblages were also detected that could be attributed to differences in host geography and diet. All trophic functional guilds (Grazers, Predators, and Intracellular Parasites) were observed, and significant correlations (α=0.05) between functional guilds were concordant with expected trophic interactions. Overall, our findings support a role for non-human primates as reservoirs of microbial eukaryotic diversity, and suggest that primate-associated microbial eukaryotic communities may follow ecological processes similar to those of free-living systems.